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Merge pull request #49 from nf-core/local-module-proseg
Local module proseg
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‎modules/local/proseg/main.nf

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process PROSEG {
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tag "$meta.id"
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label 'process_high'
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container "nf-core/proseg:1.1.8"
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input:
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tuple val(meta), path(transcripts)
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output:
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tuple val(meta), path("cell-polygons.geojson.gz"), emit: cell_polygons_2d
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path("expected-counts.csv.gz"), emit: expected_counts
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path("cell-metadata.csv.gz"), emit: cell_metadata
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path("transcript-metadata.csv.gz"), emit: transcript_metadata
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path("gene-metadata.csv.gz"), emit: gene_metadata
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path("rates.csv.gz"), emit: rates
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path("cell-polygons-layers.geojson.gz"), emit: cell_polygons_layers
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path("cell-hulls.geojson.gz"), emit: cell_hulls
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path("versions.yml"), emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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// Exit if running this module with -profile conda / -profile mamba
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if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
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error "PROSEG module does not support Conda. Please use Docker / Singularity / Podman instead."
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}
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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def platform = preset ? "${params.preset}" : ""
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// check for preset values
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if (!(platform in ['xenium', 'cosmx', 'merscope'])) {
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error "${platform} is an invalid platform (preset) type. Please specify xenium, cosmx, or merscope"
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}
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"""
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proseg \\
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--${preset} \\
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${transcripts} \\
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--nthreads ${task.cpus} \\
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--output-expected-counts expected-counts.csv.gz \\
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--output-cell-metadata cell-metadata.csv.gz \\
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--output-transcript-metadata transcript-metadata.csv.gz \\
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--output-gene-metadata gene-metadata.csv.gz \\
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--output-rates rates.csv.gz \\
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--output-cell-polygons cell-polygons.geojson.gz \\
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--output-cell-polygon-layers cell-polygons-layers.geojson.gz \\
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--output-cell-hulls cell-hulls.geojson.gz \\
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${args}
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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proseg: \$(proseg --version | sed 's/proseg //')
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END_VERSIONS
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"""
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stub:
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// Exit if running this module with -profile conda / -profile mamba
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if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
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error "PROSEG module does not support Conda. Please use Docker / Singularity / Podman instead."
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}
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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"""
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touch expected-counts.csv.gz
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touch cell-metadata.csv.gz
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touch transcript-metadata.csv.gz
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touch gene-metadata.csv.gz
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touch rates.csv.gz
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touch cell-polygons.geojson.gz
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touch cell-polygons-layers.geojson.gz
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touch cell-hulls.geojson.gz
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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proseg: \$(proseg --version | sed 's/proseg //')
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END_VERSIONS
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"""
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}

‎modules/local/proseg/meta.yml

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name: "proseg"
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description: Probabilistic cell segmentation for in situ spatial transcriptomics
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keywords:
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- segmentation
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- cell segmentation
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- spatialomics
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- probabilistic segmentation
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- in situ spatial transcriptomics
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tools:
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- "proseg":
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description: "Proseg (probabilistic segmentation) is a cell segmentation method for in situ spatial transcriptomics. Xenium, CosMx, and MERSCOPE platforms are currently supported."
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homepage: "https://github.com/dcjones/proseg/tree/main"
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documentation: "https://github.com/dcjones/proseg/blob/main/README.md"
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tool_dev_url: "https://github.com/dcjones/proseg"
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doi: ""
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licence: ["GNU Public License"]
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input:
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- - meta:
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type: map
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description: |
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Groovy Map containing run information
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e.g. `[ id:'run_id']`
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- transcripts:
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type: file
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description: |
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File containing the transcript position
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pattern: "transcripts.csv.gz"
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output:
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- - meta:
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type: map
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description: |
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Groovy Map containing run information
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e.g. `[ id:'run_id']`
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- cell_polygons:
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type: file
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description: 2D polygons for each cell in GeoJSON format. These are flattened from 3D
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pattern: "cell-polygons.geojson.gz"
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- - expected_counts:
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type: file
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description: cell-by-gene count matrix
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pattern: "expected-counts.csv.gz"
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- - cell_metadata:
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type: file
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description: Cell centroids, volume, and other information
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pattern: "cell-metadata.csv.gz"
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- - transcript_metadata:
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type: file
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description: Transcript ids, genes, revised positions, assignment probability
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pattern: "transcript-metadata.csv.gz"
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- - gene_metadata:
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type: file
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description: Per-gene summary statistics
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pattern: "gene-metadata.csv.gz"
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- - rates:
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type: file
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description: Cell-by-gene Poisson rate parameters
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pattern: "rates.csv.gz"
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- - cell_polygon_layers:
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type: file
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description: A separate, non-overlapping cell polygon for each z-layer, preserving 3D segmentation
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pattern: "cell-polygons-layers.geojson.gz"
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- - cell_hulls:
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type: file
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description: Convex hulls around assigned transcripts
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pattern: "cell-hulls.geojson.gz"
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- - versions:
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type: file
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description: File containing software versions
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pattern: "versions.yml"
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authors:
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- "@khersameesh24"
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maintainers:
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- "@khersameesh24"

‎modules/local/proseg/preprocess/main.nf

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process PROSEG2BAYSOR {
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tag "$meta.id"
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label 'process_high'
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container "nf-core/proseg:1.1.8"
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input:
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path(transcript_metadata)
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path(cell_polygons)
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output:
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path("xr-transcript-metadata.csv"), emit: xr_metadata
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path("xr-cell-polygons.geojson"), emit: xr_polygons
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script:
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// Exit if running this module with -profile conda / -profile mamba
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if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
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error "PROSEG2BAYSOR (preprocess) module does not support Conda. Please use Docker / Singularity / Podman instead."
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}
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"""
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proseg-to-baysor \
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${transcript_metadata} \
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${cell_polygons} \
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--output-transcript-metadata xr-transcript-metadata.csv \
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--output-cell-polygons xr-cell-polygons.geojson
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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proseg: \$(proseg --version | sed 's/proseg //')
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END_VERSIONS
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"""
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stub:
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// Exit if running this module with -profile conda / -profile mamba
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if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
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error "PROSEG module does not support Conda. Please use Docker / Singularity / Podman instead."
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}
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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"""
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touch xr-transcript-metadata.csv
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touch xr-cell-polygons.geojson
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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proseg: \$(proseg --version | sed 's/proseg //')
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END_VERSIONS
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"""
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}
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‎modules/local/proseg/tests/main.nf.test

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nextflow_process {
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name "Test Process PROSEG"
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script "../main.nf"
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process "PROSEG"
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tag "modules"
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tag "modules_nfcore"
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tag "proseg"
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tag "segmentation"
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tag "cell_segmentation"
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setup {
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run("UNZIP") {
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script "modules/nf-core/unzip/main.nf"
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process {
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"""
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input[0] = [[], file('https://raw.githubusercontent.com/nf-core/test-datasets/spatialxe/Xenium_Prime_Mouse_Ileum_tiny_outs.zip', checkIfExists: true)]
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"""
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}
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}
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}
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test("proseg - transcripts.csv") {
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when {
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process {
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"""
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input[0] = Channel.of([
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[id: "test_run_proseg"],
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]).combine(UNZIP.out.unzipped_archive.map { it[1] } + "/transcripts.csv")
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"""
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}
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}
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then {
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assertAll(
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{ assert process.success },
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{ assert snapshot(process.out).match() },
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{ assert file(process.out.expected_counts.get(0).get(1).find { file(it).name == 'expected-counts.csv.gz' }).exists() },
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{ assert file(process.out.cell_metadata.get(0).get(1).find { file(it).name == 'cell-metadata.csv.gz' }).exists() },
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{ assert file(process.out.transcript_metadata.get(0).get(1).find { file(it).name == 'transcript-metadata.csv.gz' }).exists() },
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{ assert file(process.out.gene_metadata.get(0).get(1).find { file(it).name == 'gene-metadata.csv.gz' }).exists() },
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{ assert file(process.out.rates.get(0).get(1).find { file(it).name == 'rates.csv.gz' }).exists() },
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{ assert file(process.out.cell_polygons.get(0).get(1).find { file(it).name == 'cell-polygons.geojson.gz' }).exists() },
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{ assert file(process.out.cell_polygons_layers.get(0).get(1).find { file(it).name == 'cell-polygons-layers.geojson.gz' }).exists() },
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{ assert file(process.out.cell-hulls.get(0).get(1).find { file(it).name == 'cell-hulls.geojson.gz' }).exists() },
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)
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}
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}
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test("proseg stub") {
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options "-stub"
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when {
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process {
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"""
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input[0] = Channel.of([
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[id: "test_run_proseg"],
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]).combine(UNZIP.out.unzipped_archive.map { it[1] } + "/transcripts.csv")
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"""
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}
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}
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then {
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assertAll(
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{ assert process.success },
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{ assert snapshot(process.out).match() }
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)
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}
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}
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}

‎modules/local/proseg/tests/tags.yml

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proseg:
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- "modules/nf-core/proseg/**"

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